ArticleProceedings of the National Academy of Sciences of the United States of America2008
Two-dimensional infrared spectra reveal relaxation of the nonnucleoside inhibitor TMC278 complexed with HIV-1 reverse transcriptase.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
45 citing papers in PubMed, 136 citations in OpenAlex.
- Structural Characterization of Fluorescent Proteins Using Tunable Femtosecond Stimulated Raman Spectroscopy.International journal of molecular sciences · 2023Article
- Delineating Ultrafast Structural Dynamics of a Green-Red Fluorescent Protein for Calcium Sensing.Biosensors · 2023Article
- Transparent window 2D IR spectroscopy of proteins.The Journal of chemical physics · 2021Review
- Protein Dynamics by Two-Dimensional Infrared Spectroscopy.Annual review of analytical chemistry (Palo Alto, Calif.) · 2021Article
- Multiple Target Drug Design Using LigBuilder 3.Methods in molecular biology (Clifton, N.J.) · 2021Article
- 2D-IR studies of cyanamides (NCN) as spectroscopic reporters of dynamics in biomolecules: Uncovering the origin of mysterious peaks.The Journal of chemical physics · 2020Article
- Unperturbed Detection of the Dynamic Structure in the Hydrophobic Core of Trp-Cage via Two-Dimensional Infrared Spectroscopy.The journal of physical chemistry letters · 2020Article
- Paired Spectroscopic and Crystallographic Studies of Proteases.ChemistrySelect · 2019Article
- Site-Specific 1D and 2D IR Spectroscopy to Characterize the Conformations and Dynamics of Protein Molecular Recognition.The journal of physical chemistry. B · 2019Article
- Excited State Structural Evolution of a GFP Single-Site Mutant Tracked by Tunable Femtosecond-Stimulated Raman Spectroscopy.Molecules (Basel, Switzerland) · 2018Article
- Synthesis of 5-Cyano-Tryptophan as a Two-Dimensional Infrared Spectroscopic Reporter of Structure.Angewandte Chemie (International ed. in English) · 2018Article
- Watching Proteins Wiggle: Mapping Structures with Two-Dimensional Infrared Spectroscopy.Chemical reviews · 2017Review
- Fermi resonance as a means to determine the hydrogen-bonding status of two infrared probes.Physical chemistry chemical physics : PCCP · 2017Article
- Two-Dimensional Infrared Study of Vibrational Coupling between Azide and Nitrile Reporters in a RNA Nucleoside.The journal of physical chemistry. B · 2016Article
- Site-specific infrared probes of proteins.Annual review of physical chemistry · 2015Review
- 2D IR spectroscopy of histidine: probing side-chain structure and dynamics via backbone amide vibrations.The journal of physical chemistry. B · 2014Article
- Snapshot of the equilibrium dynamics of a drug bound to HIV-1 reverse transcriptase.Nature chemistry · 2013Article
- Relationship of femtosecond-picosecond dynamics to enzyme-catalyzed H-transfer.Topics in current chemistry · 2013Review
- Protein dynamics studied with ultrafast two-dimensional infrared vibrational echo spectroscopy.Accounts of chemical research · 2012Article
- Conformational dynamics and stability of HP35 studied with 2D IR vibrational echoes.Journal of the American Chemical Society · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
The two nitrile groups at the wings of the nonnucleoside HIV-1 reverse transcriptase (RT) inhibitor TMC278 are both identified in high-sensitivity 2D IR spectroscopy experiments of the HIV-1 RT/TMC278 complex. The vibrational spectra indicate that the two arms of the inhibitor sense quite different environments within the hydrophobic pocket. The vibrational relaxation of the two arms are almost equal at 3 ps from model studies. The 2D IR spectra expose a significant distribution of nitrile frequencies that diffuse at equilibrium on ultrafast time scales ranging from hundreds of femtoseconds to tens of picoseconds. The slow spectral diffusion of the cyanovinyl arm of the inhibitor is attributed to its interaction with the backbone and side chains in the hydrophobic tunnel. The results show that the inhibitor cyano modes lose memory of their structural configurations relative to the hydrophobic pocket within tens of picoseconds. The cross-peaks between the two arms of the drug are tentatively attributed to relaxation of the nitrile state with both arms excited.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.